I am having the same problem! MBP 15, 8 GB, Early 2011, ML 10.8.2 and updating to Xcode 4.5.1
1. Started up in Safe Mode, but could not update from Appstore. No update available.
2. Tried from the list with all my Apps. Got message that update was availiable for an other ID. I have never changed it!
3. So, I logged in as developer and installed from there. I did OK!
4. Restarted normaly and checked App-store, and still got info that there is Xcode update 4.5.1 to be applied.
5. So I did, and after about 30 minutes, it did complete OK!
I think it was the Safe Mode installation that solved the(my) problem. The last installation from App Store, probably only checked and found out that the installation allready was done! So now App Store reallity might be true! On my machine anyway!
I will now try it on my backupsystem. (Carbon Copy Clone on a extarnal FW-800-disk).
I think It's a misstake to mix System-updates with App-updates. Apple might come back on this one, but now they are to busy working wirh the TimeMachine - Spoligth problem! ;-))